


Sometimes the Only Way Out is Through

by Sciencelings



Category: Iron Man (Movies), Marvel Cinematic Universe, Spider-Man (Tom Holland Movies)
Genre: Angst with a Happy Ending, BAMF Peter Parker, But not that much, Comedy, Comic Book Science, Coming Out, Elements of Crack, Fluff and Angst, Gen, Irondad Fic Exchange 2019, Kidnapped Peter Parker, Kidnapping, Medical Inaccuracies, Parent Tony Stark, Peter Parker Whump, Protective Tony Stark, Tony Stark Acting as Peter Parker's Parental Figure, Tony Stark Has A Heart, Trans Male Character, Trans Peter Parker, Transphobia, Whump, Worried Tony Stark, i don't deal well with whump stuff so..., the inherent fear of being socialised as a female, this is the nicest kidnapping fic you'll ever read i promise, throw away villain
Language: English
Status: Completed
Published: 2019-12-27
Updated: 2019-12-27
Packaged: 2021-02-26 07:07:41
Rating: Teen And Up Audiences
Warnings: Graphic Depictions Of Violence
Chapters: 1
Words: 4,790
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/21989263
Author URL: https://archiveofourown.org/users/Sciencelings/pseuds/Sciencelings
Summary: Peter gets kidnapped by one of his mentor's old enemies who only knows him as Tony's closest thing to a son. He doesn't know that Peter is Spider-Man. But he knows a secret that Tony doesn't and if it's revealed, it could change everything.
Relationships: Peter Parker & Tony Stark
Comments: 11
Kudos: 274
Collections: Irondad Fic Exchange 2019





	Sometimes the Only Way Out is Through

**Author's Note:**

  * For [trichoglossus](https://archiveofourown.org/users/trichoglossus/gifts).



Peter wasn’t sure why he was still afraid to walk alone at night. He was spider-man, he could handle anyone who tried to mug him or… anything else. His enhanced senses only made it worse. He could hear the footsteps a hundred feet behind him and his spider-sense was going off for no reason and overall, it was not a good time. It didn’t help that he had run out of web-fluid during patrol and was stuck on the ground until he could make more. 

It was one of those dark nights that made him feel like there was something behind every corner. The fear alone made him anxiously play with his keychain as if he could use his apartment key as some sort of knife to defend himself. He was enhanced, he didn’t need a weapon, but it was just one of those days where he wasn’t sure it would be enough. 

For some reason, his senses focused on a single car behind him. It sounded big but not like a bus big. Maybe like a large truck. Peter couldn’t hear the normal buzz of its lights. Maybe that’s what was making him uneasy. It seemed to be trying to sneak up on him. He gripped his keys tighter. Would they be sharp enough to do anything? Maybe with whatever enhanced force he had he could do some damage, but he had no reason to think that anything was going to happen. 

He really should listen to his instincts more. 

It was right before he was able to enter his apartment building when his spider-sense went from a dull ever-present buzz to a sudden peak of pain behind his skull. He ducked far earlier than he found out why, barely processing the projectile that zipped past him like a bullet. He spared a glance at the object embedded in the brick wall behind him. It looked like some sort of tranquilizer. 

Peter whipped his head around, looking for an attacker and was met with a blizzard of tranquilizers. He did his best to sprint away from the invisible assailant, but it was impossible to dodge all of the bullets. It only took a moment to take him down. He may have yelped and exclaimed a couple of curse words but nobody was able to hear.

He had been shot before, he was bound to with all the armed criminals in the city, but this was different. It wasn’t nearly as painful. Peter really didn’t like what all of that implied. Tranquilizers, getting him while he was alone, targeting him in particular, none of that could lead to anywhere good. 

Peter’s vision was fading but his hearing left a little slower. He heard some metallic sounds before a voice broke through the fog. 

“This is Stark’s kid? I thought the ‘smartest person in the world’ would choose someone at least a little smart to carry his legacy…” the voice was dripping with poison and Peter didn’t know that anyone could hate someone so much that just the feeling in his voice made Peter almost shiver. If he could move. 

“It’s him. Stark is practically attached to the kid, it took us weeks to get him without some sort of tracker attached to him.” Another voice said as Peter was hit suddenly with the tranquilizer. He was out before he could take another breath. The last thing he felt before the darkness overtook him was hope because Mr. Stark put trackers in everything he made, so he would know that something was wrong. 

Tony, however, took a little while to realize anything was up. He glanced away from Peter’s GPS location once he saw the kid was in front of his apartment building and went back to correcting some of Peter’s work that he had done that day. He would check again later to see if he was going on patrol but at this point, he thought that Spider-Man could hold his own. 

Peter woke up long before he was supposed to. It took a minute to force himself out of the foggy feeling of the drugs. He felt cold metal around his wrists and he was sat upright in a chair straight out of a sci-fi villains lair. It held all of his limbs tightly against its blocky frame and Peter swore there was a light above his head even though he couldn’t move his head anywhere. 

Peter pretended to be asleep for a few minutes while he gathered as much information as he could with his eyes closed. Not because he was absolutely terrified and unable to face the reality of his situation. Definitely not that. 

There were voices coming from… somewhere, but they were far away and muffled, he couldn’t make out a single word. But that could have also been from all the drugs that his body was struggling to purify himself of. 

He also noticed that the room was really fucking cold. Ever since he got bitten by the spider he had a problem with the cold and this was really solidifying the fact that he hated the cold. This was terrible, he wanted to leave. 

He tested his restraints, which were just handcuffs connected to the arms of the chair. They didn’t feel like anything special, he felt them slightly bend with enough pressure. He could probably break out pretty easily, but he knew that that wouldn’t fix all his problems. He could sense armed guards everywhere. As his senses cleared from the drugs, he could hear the clicking of metal and other classic gun sounds. He was pretty familiar with gun sounds. He was a vigilante working in America of fucking course he was hyper-aware of what guns sounded like. 

He had just begun to calm himself down and start thinking like a rational person when the sound of footsteps and the familiar, unhinged voice approached his concrete room. He felt himself stiff up as the noise got louder and louder until there was a loud bang at the steel door that made him flinch. 

“Oh, Petey!” The guy with the crazy voice said in a sing-song voice followed by a cackle as he burst into the room. He ended up looking a little more normal than Peter had imagined. He thought the crazy guy would end up looking like a Batman villain. He was just bald despite looking youngish and his eyes looked a little off like he was absolutely batshit but was trying his hardest to look normal. 

“What do you want with me?” Peter’s voice shook a little against his will. Goddammit, he just wanted to sound brave and now that was out the window. 

“Don’t worry kiddie, this isn’t personal. I’m just seeking a little bit of revenge!” 

“How is kidnapping me not personal…” 

“It’s not about you… it’s about Stark! And what better way to hurt him than through you! You are the most vulnerable of his playthings…” 

“Why… What did he do to you?” 

“Oh this isn’t about what he did to me, I mean, he killed my father, but that’s not why I’m doing this. He’s weak, he has limits. Limits that I myself have broken in the name of technological advancement for the good of all mankind. He still depends on a suit… why wear a machine when you can be the machine.” The man cackled. “But I plan to have some fun, why not make a little mess in the progress right?” 

“What do you mean…” 

“We’ve been watching you Pete, we know that you have some secrets that it would be… entertaining to reveal. I’m sure we can change everything you know with just one of them.” This made Peter pause. Did they know he was Spider-Man? If they did, he was sure they’d tie him down a little harder. So was it the other thing? There weren’t many big things he hasn’t told Mr. Stark except for… oh. Somehow they must know he’s trans. It was the one big secret that Tony didn’t know that Peter was slightly worried about him knowing. Peter never knew how boomers would react to things like that. It was kind of a wild card. 

Peter felt that familiar rush of fear in his chest, the same one he had felt when May found out he cut his hair with scissors in junior high, or when Flash started going after him for ‘dressing like a boy’. The same terror that engulfed him when Ned convinced him to tell Ben and May. He already loved his relationship with Tony as it was, without him knowing. He didn’t want to change anything. He really didn’t want Mr. Stark to look at him any differently. He was satisfied with the way things were. 

“Ah, that was the reaction I really hoped you’d have!” He must not have been hiding his fear very well as the Batman villain guy grinned eerily. 

“Before we go any further, I apologize, I haven’t even told you who I am! It could shed some light for you. My name is Ezekiel Stane.”

“Stane like Obadiah? Like that asshole that got Tony kidnapped and stole his technology to attempt to kill him several times… Okay first of all, someone willingly fucked him? Like ew. That guy was totally evil villain material you could tell. Is that like a bald-people thing? Is that why you’re doing this?” 

“I was told you were smart… it doesn’t seem very smart to say those types of things when you are handcuffed to a chair. I can do anything I want to you and you wouldn’t be able to do anything. I would advise that you watch your mouth.” Ezekiel hissed. “Now there’s no reason to waste any more time, we have a call to make.” 

***

Tony was in the process of getting dragged out of his lab by his fiance when FRIDAY set off an alarm. Not the one that signaled that someone was trying to break into his penthouse, but one that signaled that something was wrong with Spider-Man. It was an alarm he was used to hearing but never ceased to give him a violent ping of terror that made his chest hurt. 

Pepper froze in place as she knew that she wouldn’t be able to drag Tony away when Peter was in trouble. She didn’t really want to anyway, she was worried about the kid too. 

The alarm was set off by a video call, not an alert from Karen or May calling to tell him that Peter had failed to come home. Tony didn’t spare a second to answer. He was right to dread what he would see. 

The image vaguely familiar man in a plain concrete room popped up on the largest holoscreen. The man was familiar in the way an elementary school bully was recognized so many years later. Tony took a while to realize who it was. 

“Good morning Stark! It is morning isn’t it? I feels early enough to be morning…” the man rambled manically. It was obvious that there was something wrong with him. An insane glint in his eyes, the way his head twitched, the way his fingers tapped against his leg, the pitches of his voice. Tony knew this guy wasn’t mentally sound. 

“How did you get past Friday?” Tony narrowed his eyes as the man waved the question away.

“It doesn’t matter, I haven’t even introduced myself. How rude of me. Dear dad would’ve been so disappointed. I’m Ezekiel. Ezekiel Stane.”

“Obie fucked?” Tony said, obviously shocked at the revelation. 

“That’s what I said!” exclaimed a horrifyingly familiar young voice from the other side of the video transmission. 

“Kid?” he said, much more worried this time.

“You just had to ruin the surprise! Where’s your sense of drama!” Ezekiel exclaimed in agony, not even acknowledging the insult against his late father. “Fine, I kidnapped your stupid intern, I really shouldn’t have to go so far to catch your attention…” 

“Peter, did he hurt you?” 

“I’m fine! Just a little cold.” 

“Thank god…”

“Hello? Asshole? I kidnapped your kid, at least act a little more reasonable.” Ezekiel hissed. 

“Why do you think I’m stalling for so long, I had to have enough time to track your call.” 

“You think I’m so stupid to let you have a way to track our location? I am entirely more advanced than anything you have ever created in every-” 

“Pardon the interruption but I have found their location.” Friday announced pleasantly. From what Tony could see, she had analyzed the visual location of the video and combined that with her algorithm for possible places it could be. She narrowed down the place based on where it was possible for them to be in the time Peter had been gone and where the call was transmitting from. Stane had tried to block the signal but had only managed to expand the search area a few miles. Visual clues narrowed it down completely. The guy was a little crazy, he was bound to have overlooked a few holes in his plan. 

“Good, I’ll be right there Peter! Don’t to anything stupid until I get there!” Tony turned to Pepper who had remained quiet this entire time. “You know what to do?” 

“You know this isn't my first rodeo. Come back safe,” Pepper requested. They acted as if the situation was something normal and casual as they knew if one of them freaked out, the other would as well and that probably wasn’t going to help Peter. 

“See you soon egghead!” 

***

Peter had been left alone in the cold room for a little while, he had noticed that his captor was more positive than he was expecting, with his plan foiled and all. It made Peter suspicious. 

He knew Tony said to not do anything stupid until he got there but he was uncomfortable and the metal on the handcuffs were getting cold, so he broke them. He ripped them off of the arms of the chair and bend the metal until they broke. He stood up and stretched before considering his options. 

He decided on the element of surprise.

After waiting for several long minutes, Peter heard a little bit of a commotion in the hallways. Echoing gunshots, yelling, all that fun stuff. He smiled when he heard the familiar sound of charging repulsors and his mentors grumpy voice behind the metal mask. 

Peter had just stuck himself to the ceiling when the door was blasted in. A suit that definitely wasn’t Tony’s walked in. It was white and dark red, like the color of old blood. It had big round glowing eyes and a horizontal rectangular power source on the chest. It was pretty ugly. 

“What-” Ezekiel's metallic voice exited the discount iron man before being blasted back by the Gucci one. 

“Hey Mr. Stark!” Peter called the attention of both metal people, who looked up at him with unreadable expressions, as they had masks on. But Peter imagined that Ezekiel was a little shocked. 

“Hey kid, you good?” Tony asked while the off brand metal guy seemed to gawk. But again, Peter could see his face, so he didn’t know. 

“Yeah. Can we go now?” Peter dropped and gracefully landed on his feet. 

“In a minute, I still have to take care of this guy.” 

It turned out that Bootleg Iron Man wasn’t just standing there in shock. Peter figured this out when the suit came off. Well, it didn’t exactly come off. It seemed to go inside his skin like he was reverse sweating. It was actually pretty gross. It was even more gross when it oozed out of his palms and covered the concrete walls of the solitary room. 

White and red metallic liquid bubbled on the walls as spikes formed, pointing towards Peter and Tony. The metal solidified after repulser-like blue lights were revealed on the ends of the spikes. They didn’t leave much room to move. The strange metal even sheilded Ezekiels dumb smug face from them. Then, the recently created turrets started shooting at them. 

At this point, time seemed to both slow down and speed up, if that makes any sense. Maybe it was the sudden chaos mixed with his spider-sense that made time seem inconsistent but it didn’t really matter why it was happening. 

Peter didn’t think Tony could move so fast. The iron man suit opened up and Tony burst out as the sound of the the first blaster revved up with a high pitched squeal. He shielded as much of Peter’s body as he could with the empty iron suit doing the same to the opposite side. Even with his powers, Peter froze for a moment in shock. Not a long enough moment for the blasts to go off, but it felt longer than it was. 

His spider sense kicked up a notch when the spike right behind Tony grew at an alarming rate, moments from impaling him. Peter pushed Tony out of the way and punched the spike with all his might. It didn’t bend, it didn’t make a dent, it fucking shattered like glass. The shards of metal just melted back into the ever moving structure of the room. 

“Stane is controlling this shit right? We need to find him and take him out!” Peter said frantically. “Get back in the suit.” 

“But you don’t have any armor-”

“Sorry old man, but I’m a little more durable than you are.”Tony seemed to protest so Peter killed two birds with one stone and pushed his mentor into the open shell of the suit as an energy blast barely missed him. The blasts were few and not the best at aiming but they were extremely powerful. Peter could tell by the way a single shot had almost ripped off an arm of the iron suit. 

“If you get shot because of this I’m going to be pissed.” 

“I know. We need to get through the walls, he has to be behind there somewhere.” Peter said as he ripped one of the spikes off of the wall and hurled it at the one that was growing behind him. Tony just grumbled and shot his repulsors at the turrets. His blasts didn’t do as much damage as Peter’s fists but they did enough. The metal making up everything in the room was surprisingly brittle and had a low melting point, he assumed it was so it would be more malleable when Ezekiel controlled it with his crazy brain. 

“If you cover me for a minute, I think I can blast us out of here.” Tony said as he aimed his fist at the ceiling and turned on his powerful laser. Peter remembered it from the ferry incident. He ignored the pang of cringe that came with the memory and sprung from wall to wall, breaking spikes and smashing things. It kind of felt good to just break things, maybe that was just the mentality of the Hulk coming through. 

Right before Tony had finished burning a hole in the metal above them, Peter got blasted. One of the fixed repulsors caught his leg and he went flying into the opposite wall with a yelp. Tony stopped playing with his laser and surged towards Peter.

“I’ve got you kid-” He muttered as he picked Peter up with one of his armored arms and shot a tiny missile at the sky, completing their escape hole. Tony held Peter close as he changed them through the falling debris.

There was a moment of silence as they hovered above the smoking building. They sighed simultaneously when a figure rose from the crumbling opening. Ezekiel had his armor on, sans his helmet, maybe for dramatic effect, maybe because he was the stupidest genius that had ever lived. Peter couldn’t tell. 

“We haven’t even gotten to the good part yet!” Ezekiel shrieked. “I’ve only been able to tease the boys secret!” his voice spat out the word ‘boy’ as if it was a horrible slur. 

“That’s not your secret to tell dipshit.” Peter grumbed and grabbed a fist sized chunk of debris that had gotten caught between him and Tony, he threw it with all his might at the man's exposed head. It collided like a comet and just like that, the baddie was out. His suit immediately froze. It’s thrusters stopped, the glowing rectangle on the chest dimmed and he fell back into the ruins of the building. He didn’t even fly that high so Peter didn’t feel as bad. That and he could still feel the guys heartbeat so for now, he was still alive. 

“That was a little bit easier than I thought it would be…” Tony announced, a little bit surprised. He didn’t immediately notice Peter starting to go limp. Now that it was over and the adrenaline rush was fading, the pain from the blast to his leg was really coming to his attention. The pain alone was enough to bring tears to his eyes but he couldn’t find himself making a noise.

Peter’s healing factor started to kick in, he knew because of the sudden exhaustion that hit him. For some reason he healed better when he was asleep, so whenever he got hurt this bad, his body's immediate response was to go for a nap.

“Hey kid, come on, stay with me-” Tony said frantically as Peter’s vision went black. Honestly, sleeping sounded a whole lot better than being in pain. He welcomed the calm darkness without a single regret. 

***

Peter knew he had been dreaming, he knew the dream had been vivid and incredible, but he couldn’t remember much else. He could only recall a single random moment, not anything after it or before it. It was strange but not entirely abnormal. 

He spent quite a lot of time in between consciousness and a deep sleep, where there wasn’t much to feel. When he finally approached a state of awareness, he could only hear a voice. A wonderfully comforting voice. One that made him feel happy despite the waves of mild pain that were starting to pulse through him. 

He started to feel a warm pressure in his hand as if he was holding someone else's. He vaguely noticed the lack of pressure on his chest and the soft feeling of his favorite hoodie against his skin. He wasn’t exactly aware enough to connect any dots. He just enjoyed breathing freely and had a moment where he wanted to giggle at the softness of the hoodie. You know, like a completely sober and not drugged up person. 

There was a dim light behind his eyelids. He forced them open, he needed to wake up even though he was so exhausted. It was like Thor’s hammer was resting on his eyelids, they were so irrationally heavy. He just had to open them though. 

“Tony?” Peter muttered weakly. 

“Kid? You’re not supposed to be awake yet…” He said softly as he met Peter’s eyes. 

“I was a little impatient.” he smiled a little, the sleepiness floating at the back of his skull rather than pulling at his eyelids. “What happened?” 

“We got Obie jr. Turns out all of the experimental technology that he put into himself was messing with his brain and making him crazy. We’re working on a solution but keeping him in a medically induced coma in the meantime.” Mr. Stark explained, “You’re here because the crazy bitch shot your leg with an ultra-powerful energy beam. If you weren’t enhanced you probably wouldn’t even have a leg right now. Thanks to your crazy healing factor, you’re not going to be in the med bay for a year. But you aren’t allowed to walk and we’re going to keep you nice and drugged up for a little while.” 

“Fun.” Peter groaned and tried to drag himself up to a sitting up position. This was a bad decision because it fucking hurt.

“Woah there, I said no moving remember?” Tony scolded, even though he was helping Peter be comfortable. 

“Whatever, I need to tell you something…” He grunted as he settled onto the obsessive amount of pillows that were definitely Tony’s doing. 

“You don’t have to-” 

“No, I’m gonna. I should’ve told you earlier but I was afraid and I think the drugs are making me less afraid so I’m gonna tell you now.”

“If this is about what Stane said-” 

“Shut up. I’m trans. I was born with the body of a girl but I’m not a girl, I’m a boy. I never got to tell Ben and I didn’t want to ruin anything with you-” Peter went silent as he tried to figure out what he wanted to say. Tony took the opportunity to try to settle the kid’s anxieties. 

“I know it’s not easy to come out, so I didn’t say anything, but I knew. In my quest to find spider-mans identity I may have stumbled onto things that revealed the truth but I didn’t want to be that asshole that forces you out of the closet before you’re ready. I just want to know that it won’t change anything and I’m still going to worry over all of your bad decisions.” 

“You… of course you knew. What gave it away?” 

“May has an old facebook page with a ton of pictures…”

“Oh god…” Peter groaned as Tony laughed. 

“You had an awful lot of Iron Man themed things…” 

“You’ve been to my apartment, I still have an awful lot of Iron Man themed things.” Peter deadpanned. Tony huffed a laugh. “Wait, where is May?” 

“She was on night-time duty, you just happened to wake up during my shift. But you look like you’re going to fall asleep any moment so I won’t bother waking her up. She was worried but wittle baby Petey needs to sleeby.” Mr. Stark said in a baby voice as Peter just groaned knowing that Tony was right. Unconsciousness was a blessing the human race did not deserve. 

“Yeah whatever, little baby peter, haha funny joke…” Peter yawned. He wouldn’t be able to acknowledge Tony’s response to him coming out and the great relief it gave him until he was more awake and on slightly less drugs, but at this moment, he felt at peace. He had nothing more to hide, Tony was chill about it, even if he had already known beforehand. 

Peter didn’t know how much it had burdened him until it was gone. He didn’t realize how afraid he was to admit it until it was over. He didn’t realize how much effort it was to keep the secret until he didn’t have to anymore. All of the worries about ruining things and messing up and having to explain what being transgender was and imagining Tony’s face sour or look at him in disgust. 

Peter looked up at Tony’s face. The man looked tired but behind that, there was this soft energy in his eyes, even though he looked lost in his thoughts. Peter recognized the open look whenever Tony talked to Pepper or even Colonel Rhodes on the phone. It was such an intimately affectionate look that Peter was sure Tony didn’t even realize he was doing it. It was so different from the reaction he had imagined that it made his heart swell. He didn’t end up ruining the best thing that had ever happened to him and dear god it felt good. 

“Mr. Stark?”

“Yeah?” Tony tilted his head as he was brought back to reality. 

“Thank you.” Peter ignored the pain as he awkwardly launched himself to hug his mentor. He did this partially because he didn’t want Tony to see the tears that had decided to pool in his eyes. He did it mostly because he really really needed it. He relaxed in Tony’s arms as he had never felt safer. 

Tony’s hand wandered subconsciously through Peter’s hair and didn’t even realize that he had fallen asleep in his arms until he heard the kids soft snoring. He huffed an amused laugh and just held him for a little while longer. No one was looking and it was such a relief that the kid was okay that he just enjoyed the physical proof. He was safe and back where he was supposed to be. 

The next day May would try to make a trans flag themed cake but mess it up enough that Happy would have to order one. They would bring Peter his favorite ice cream from his favorite place, they would watch every star wars way too many times that week, but for now, Peter was in Tony’s arms. Safe and snoring. 

Right where he’s supposed to be.

**Author's Note:**

> I know I haven't updated other fics in a while but now that this project is done, I can do that. Eventually. I'm trying lol. If you like this, please leave a comment, I had a lot of fun writing this, it's not exactly something that I would normally do and I'm happy for the opportunity. I have big plans for the future of my writing and would love to have anyone come along for the ride. Happy Holidays!
> 
> PS. I need attention. Comments are highly valued to a little writer like me.


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